Exploiting Overlapping Advantages of in vitro and in cellulo Selection Systems to Isolate a Novel High-affinity cJun Antagonist

We have combined two peptide library-screening systems, exploiting the benefits
offered by both to select novel antagonistic agents of cJun. CIS display is an in vitro cell-free system that allows very large libraries (≤1014) to be interrogated. However, affinity-based screening conditions can poorly reflect those relevant to therapeutic application, particularly for difficult intracellular targets, and can lead to false positives. In contrast, an in cellulo screening system such as the Protein-fragment Complementation Assay (PCA) selects peptides with high target affinity while additionally profiling for target-specificity, protease resistance, solubility and lack of toxicity in a more relevant context. A disadvantage is the necessity to transform cells, limiting library sizes that can be screened to ≤106. However, by combining both cell-free and cell-based systems, we isolated a peptide (CPW) from a ~1010 member library, which forms a highly stable interaction with cJun (Tm 63 °C, Kd 750 nM, ΔG -8.2 kcal/mol) using the oncogenic transcriptional regulator AP-1 as our exemplar target. In contrast, CIS display alone, selected a peptide with low affinity for cJun (Tm 34 °C, Kd 25 μM, ΔG -6.2 kcal/mol), highlighting the benefit of CIS→PCA. Furthermore, increased library size with CIS→PCA allows the freedom to introduce non-canonical options, such as interfacial aromatics, and solvent exposed options that may allow the molecule to explore alternative structures and interact with greater affinity and efficacy with the target. CIS→PCA therefore offers significant potential as a peptide-library screening platform by synergistically combining the relative attributes of either assay to generate therapeutically interesting compounds that may otherwise not be identified.